How do you use two patches simulataneously with ab initio folding?

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    • December 21, 2011 at 11:24 pm #1124
      Anonymous

        I tried to use replonly and phosphorylation patches together but couldn’t get the simulation to work. The program only recognizes the 1st declared patch.

        Any suggestions?

      • December 22, 2011 at 12:46 am #6458
        Anonymous

          Try out:level instead of run:level for the big list o’ patches.

          Looking at the code directly, it seems to me they should combine fine. Did you try both permutations?

          I’ve cc’ed one of the devs about reponly.

        • December 30, 2011 at 1:12 am #6480
          Anonymous

            I wonder did you get the phosphorylated patch work stand alone? The ser_phosphorylated.txt cannot be called by using -patch_selectors since it doesn’t has CMDLINE_SELECTOR inside that. So the question now is how to use ser_phophorylated.txt patch. Anyone?

          • December 22, 2011 at 12:58 am #6459
            Anonymous

              I dug into it more and replonly doesn’t make named patches, so Ray’s input is definitely needed…

            • December 23, 2011 at 11:43 pm #6471
              Anonymous

                Yes, I did. Same problem.

              • December 30, 2011 at 3:18 am #6481
                Anonymous

                  Have you tested whether your pdb has the ser_phosphorylated.txt patch created? Also, since this ser_phosphorylated.txt patch is to be read by Rosetta in default, you don’t need to specify that using -patch_selectors as you used for replonly.

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